Toward improved calibration of hydrologic models: Combining the strengths of manual and automatic methods

Automatic methods for model calibration seek to take advantage of the speed and power of digital computers, while being objective and relatively easy to implement. However, they do not provide parameter estimates and hydrograph simulations that are considered acceptable by the hydrologists responsible for operational forecasting and have therefore not entered into widespread use. In contrast, the manual approach which has been developed and refined over the years to result in excellent model calibrations is complicated and highly labor-intensive, and the expertise acquired by one individual with a specific model is not easily transferred to another person (or model). In this paper, we propose a hybrid approach that combines the strengths of each. A multicriteria formulation is used to "model" the evaluation techniques and strategies used in manual calibration, and the resulting optimization problem is solved by means of a computerized algorithm. The new approach provides a stronger test of model performance than methods that use a single overall statistic to aggregate model errors over a large range of hydrologic behaviors. The power of the new approach is illustrated by means of a case study using the Sacramento Soil Moisture Accounting model

Toward improved calibration of hydrologic models: Multiple and noncommensurable measures of information

Several contributions to the hydrological literature have brought into question the continued usefulness of the classical paradigm for hydrologic model calibration. With the growing popularity of sophisticated 'physically based' watershed models (e.g., landsurface hydrology and hydrochemical models) the complexity of the calibration problem has been multiplied many fold. We disagree with the seemingly widespread conviction that the model calibration problem will simply disappear with the availability of more and better field measurements. This paper suggests that the emergence of a new and more powerful model calibration paradigm must include recognition of the inherent multiobjective nature of the problem and must explicitly recognize the role of model error. The results of our preliminary studies are presented. Through an illustrative case study we show that the multiobjective approach is not only practical and relatively simple to implement but can also provide useful information about the limitations of a model

NiftyNet: a deep-learning platform for medical imaging

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.Comment: Wenqi Li and Eli Gibson contributed equally to this work. M. Jorge Cardoso and Tom Vercauteren contributed equally to this work. 26 pages, 6 figures; Update includes additional applications, updated author list and formatting for journal submissio

Toward improved identifiability of hydrologic model parameters: The information content of experimental data

We have developed a sequential optimization methodology, entitled the parameter identification method based on the localization of information (PIMLI) that increases information retrieval from the data by inferring the location and type of measurements that are most informative for the model parameters. The PIMLI approach merges the strengths of the generalized sensitivity analysis (GSA) method [Spear and Hornberger, 1980], the Bayesian recursive estimation (BARE) algorithm [Thiemann et al., 2001], and the Metropolis algorithm [Metropolis et al., 1953]. Three case studies with increasing complexity are used to illustrate the usefulness and applicability of the PIMLI methodology. The first two case studies consider the identification of soil hydraulic parameters using soil water retention data and a transient multistep outflow experiment (MSO), whereas the third study involves the calibration of a conceptual rainfall-runoff model

Numerical Fitting-based Likelihood Calculation to Speed up the Particle Filter

The likelihood calculation of a vast number of particles is the computational bottleneck for the particle filter in applications where the observation information is rich. For fast computing the likelihood of particles, a numerical fitting approach is proposed to construct the Likelihood Probability Density Function (Li-PDF) by using a comparably small number of so-called fulcrums. The likelihood of particles is thereby analytically inferred, explicitly or implicitly, based on the Li-PDF instead of directly computed by utilizing the observation, which can significantly reduce the computation and enables real time filtering. The proposed approach guarantees the estimation quality when an appropriate fitting function and properly distributed fulcrums are used. The details for construction of the fitting function and fulcrums are addressed respectively in detail. In particular, to deal with multivariate fitting, the nonparametric kernel density estimator is presented which is flexible and convenient for implicit Li-PDF implementation. Simulation comparison with a variety of existing approaches on a benchmark 1-dimensional model and multi-dimensional robot localization and visual tracking demonstrate the validity of our approach.Comment: 42 pages, 17 figures, 4 tables and 1 appendix. This paper is a draft/preprint of one paper submitted to the IEEE Transaction

A Diabatic Three-State Representation of Photoisomerization in the Green Fluorescent Protein Chromophore

We give a quantum chemical description of bridge photoisomerization reaction of green fluorescent protein (GFP) chromophores using a representation over three diabatic states. Bridge photoisomerization leads to non-radiative decay, and competes with fluorescence in these systems. In the protein, this pathway is suppressed, leading to fluorescence. Understanding the electronic structure of the photoisomerization is a prerequisite to understanding how the protein suppresses this pathway and preserves the emitting state of the chromophore. We present a solution to the state-averaged complete active space problem, which is spanned at convergence by three fragment-localized orbitals. We generate the diabatic-state representation by applying a block diagonalization transformation to the Hamiltonian calculated for the anionic chromophore model HBDI with multi-reference, multi-state perturbation theory. The diabatic states that emerge are charge-localized structures with a natural valence-bond interpretation. At planar geometries, the diabatic picture recaptures the charge transfer resonance of the anion. The strong S0-S1 excitation at these geometries is reasonably described within a two-state model, but extension to a three-state model is necessary to describe decay via two possible pathways associated with photoisomerization of the (methine) bridge. Parametric Hamiltonians based on the three-state ansatz can be fit directly to data generated using the underlying active space. We provide an illustrative example of such a parametric Hamiltonian